Does WinISD take into account port and driver volume?

Yes, the box volume in WinISD (and most other modelling programs) is the net volume only, so everything else still needs to be added in before you can start to calculate the external dimensions. Depending on your design you may also need to account for bracing & handles as well as the port & driver that you already mentioned.
 
Thanks! Maybe more then since I just look for [Vid], but see [now] that it's more spelled out in the mounting specs, which I 'tunnel vision' only ever look for mounting depth, so maybe whatever driver KK has is published.